Skip to content

CLI Reference

Complete command-line interface documentation.

Main Command

linkml-reference-validator [OPTIONS] COMMAND [ARGS]...

Options

  • --help - Show help message and exit

Commands

  • validate - Validate supporting text against references
  • cache - Manage reference cache

validate

Validate supporting text against references.

linkml-reference-validator validate COMMAND [ARGS]...

Subcommands

  • text - Validate a single text quote
  • data - Validate supporting text in data files

validate text

Validate a single supporting text quote against a reference.

Usage

linkml-reference-validator validate text [OPTIONS] TEXT REFERENCE_ID

Arguments

  • TEXT (required) - The supporting text to validate
  • REFERENCE_ID (required) - Reference ID (e.g., PMID:12345678)

Options

  • --cache-dir PATH - Directory for caching references (default: references_cache)
  • --verbose, -v - Verbose output with detailed logging
  • --help - Show help message

Examples

Basic validation:

linkml-reference-validator validate text \
  "MUC1 oncoprotein blocks nuclear targeting" \
  PMID:16888623

With custom cache directory:

linkml-reference-validator validate text \
  "MUC1 oncoprotein blocks nuclear targeting" \
  PMID:16888623 \
  --cache-dir /path/to/cache

With verbose output:

linkml-reference-validator validate text \
  "MUC1 oncoprotein blocks nuclear targeting" \
  PMID:16888623 \
  --verbose

With editorial notes:

linkml-reference-validator validate text \
  'MUC1 [mucin 1] oncoprotein blocks nuclear targeting' \
  PMID:16888623

With ellipsis:

linkml-reference-validator validate text \
  "MUC1 oncoprotein ... nuclear targeting" \
  PMID:16888623

Exit Codes

  • 0 - Validation successful
  • 1 - Validation failed

Output Format

Validating text against PMID:16888623...
  Text: MUC1 oncoprotein blocks nuclear targeting

Result:
  Valid: True
  Message: Supporting text validated successfully in PMID:16888623
  Matched text: MUC1 oncoprotein blocks nuclear targeting...

validate data

Validate supporting text in data files against their cited references.

Usage

linkml-reference-validator validate data [OPTIONS] DATA_FILE

Arguments

  • DATA_FILE (required) - Path to data file (YAML/JSON)

Options

  • --schema PATH, -s PATH (required) - Path to LinkML schema file
  • --target-class TEXT, -t TEXT - Target class to validate (optional)
  • --cache-dir PATH, -c PATH - Directory for caching references (default: references_cache)
  • --verbose, -v - Verbose output with detailed logging
  • --help - Show help message

Examples

Basic validation:

linkml-reference-validator validate data \
  data.yaml \
  --schema schema.yaml

With target class:

linkml-reference-validator validate data \
  data.yaml \
  --schema schema.yaml \
  --target-class Statement

With custom cache:

linkml-reference-validator validate data \
  data.yaml \
  --schema schema.yaml \
  --cache-dir /path/to/cache

With verbose output:

linkml-reference-validator validate data \
  data.yaml \
  --schema schema.yaml \
  --verbose

Exit Codes

  • 0 - All validations passed
  • 1 - One or more validations failed

Output Format

Success:

Validating data.yaml against schema schema.yaml
Cache directory: references_cache

Validation Summary:
  Total checks: 3
  All validations passed!

Failure:

Validating data.yaml against schema schema.yaml
Cache directory: references_cache

Validation Issues (2):
  [ERROR] Text part not found as substring: 'MUC1 activates JAK-STAT'
    Location: Statement

Validation Summary:
  Total checks: 3
  Issues found: 2

cache

Manage reference cache.

linkml-reference-validator cache COMMAND [ARGS]...

Subcommands

  • reference - Cache a reference for offline use

cache reference

Pre-fetch and cache a reference for offline use.

Usage

linkml-reference-validator cache reference [OPTIONS] REFERENCE_ID

Arguments

  • REFERENCE_ID (required) - Reference ID (e.g., PMID:12345678)

Options

  • --cache-dir PATH, -c PATH - Directory for caching references (default: references_cache)
  • --force, -f - Force re-fetch even if cached
  • --verbose, -v - Verbose output with detailed logging
  • --help - Show help message

Examples

Cache a reference:

linkml-reference-validator cache reference PMID:16888623

Force refresh:

linkml-reference-validator cache reference \
  PMID:16888623 \
  --force

Custom cache directory:

linkml-reference-validator cache reference \
  PMID:16888623 \
  --cache-dir /path/to/cache

Output Format

Fetching PMID:16888623...
Successfully cached PMID:16888623
  Title: MUC1 oncoprotein blocks nuclear targeting...
  Authors: Raina D, Ahmad R, Joshi MD
  Content type: abstract_only
  Content length: 1523 characters

Reference ID Formats

PubMed (PMID)

PMID:12345678
PMID:9876543
  • Numeric identifier only
  • Fetches abstract and metadata

PubMed Central (PMC)

PMC:3458566
PMC:7654321
  • Numeric identifier only
  • Fetches full-text when available

Environment Variables

LINKML_REFERENCE_VALIDATOR_CACHE_DIR

Override default cache directory:

export LINKML_REFERENCE_VALIDATOR_CACHE_DIR=/custom/cache
linkml-reference-validator validate text "..." PMID:12345678

NCBI_API_KEY

Set NCBI API key for higher rate limits:

export NCBI_API_KEY=your_api_key_here
linkml-reference-validator validate text "..." PMID:12345678

Request an API key: https://www.ncbi.nlm.nih.gov/account/settings/

Shell Integration

Exit Code Usage

if linkml-reference-validator validate text \
    "MUC1 oncoprotein blocks nuclear targeting" \
    PMID:16888623 > /dev/null 2>&1; then
  echo "✓ Valid"
else
  echo "✗ Invalid"
fi

Batch Processing

for pmid in PMID:111 PMID:222 PMID:333; do
  echo "Validating $pmid..."
  linkml-reference-validator validate text \
    "some text" \
    "$pmid"
done

Piping Output

# Save output to file
linkml-reference-validator validate text \
  "..." PMID:12345678 \
  > validation_result.txt

# Grep for specific info
linkml-reference-validator validate data \
  data.yaml \
  --schema schema.yaml \
  | grep "Valid:"

Backward Compatibility

Old hyphenated commands still work but are deprecated:

# Old (deprecated but working)
linkml-reference-validator validate-text "..." PMID:123
linkml-reference-validator validate-data data.yaml --schema schema.yaml
linkml-reference-validator cache-reference PMID:123

# New (preferred)
linkml-reference-validator validate text "..." PMID:123
linkml-reference-validator validate data data.yaml --schema schema.yaml
linkml-reference-validator cache reference PMID:123

The old commands are hidden from --help but continue to function.

See Also